HEADER ISOMERASE 03-AUG-12 4GFJ
TITLE CRYSTAL STRUCTURE OF TOPO-78, AN N-TERMINAL 78KDA FRAGMENT OF
TITLE 2 TOPOISOMERASE V
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TOPOISOMERASE V;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1-685;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: METHANOPYRUS KANDLERI AV19;
SOURCE 3 ORGANISM_TAXID: 190192;
SOURCE 4 STRAIN: AV19;
SOURCE 5 GENE: MK1436, TOPOISOMERASE V;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET14B
KEYWDS HELIX-HAIRPIN-HELIX, DNA REPAIR ENZYME, TOPOISOMERASE, DNA BINDING,
KEYWDS 2 ISOMERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR R.RAJAN,R.PRASAD,B.TANEJA,S.H.WILSON,A.MONDRAGON
REVDAT 3 13-SEP-23 4GFJ 1 REMARK
REVDAT 2 09-JAN-13 4GFJ 1 JRNL
REVDAT 1 05-DEC-12 4GFJ 0
JRNL AUTH R.RAJAN,R.PRASAD,B.TANEJA,S.H.WILSON,A.MONDRAGON
JRNL TITL IDENTIFICATION OF ONE OF THE APURINIC/APYRIMIDINIC LYASE
JRNL TITL 2 ACTIVE SITES OF TOPOISOMERASE V BY STRUCTURAL AND FUNCTIONAL
JRNL TITL 3 STUDIES.
JRNL REF NUCLEIC ACIDS RES. V. 41 657 2013
JRNL REFN ISSN 0305-1048
JRNL PMID 23125368
JRNL DOI 10.1093/NAR/GKS1017
REMARK 2
REMARK 2 RESOLUTION. 2.91 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0109
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.91
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.10
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 18292
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.205
REMARK 3 R VALUE (WORKING SET) : 0.201
REMARK 3 FREE R VALUE : 0.267
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 989
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.91
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1263
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.22
REMARK 3 BIN R VALUE (WORKING SET) : 0.2870
REMARK 3 BIN FREE R VALUE SET COUNT : 58
REMARK 3 BIN FREE R VALUE : 0.3990
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4940
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 19
REMARK 3 SOLVENT ATOMS : 4
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 35.40
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.40
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.21000
REMARK 3 B22 (A**2) : -2.21000
REMARK 3 B33 (A**2) : 3.32000
REMARK 3 B12 (A**2) : -1.11000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.413
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.312
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 35.583
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.897
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5057 ; 0.008 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 3650 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6805 ; 1.035 ; 1.994
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8794 ; 0.817 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 613 ; 5.434 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;32.614 ;22.874
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 953 ;16.226 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 68 ;16.247 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 747 ; 0.056 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5604 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1065 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3045 ; 0.282 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1239 ; 0.039 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4903 ; 0.555 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2012 ; 1.086 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1902 ; 1.584 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 6
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 3 A 217
REMARK 3 ORIGIN FOR THE GROUP (A): 33.9923 -55.6589 -3.1772
REMARK 3 T TENSOR
REMARK 3 T11: 0.1704 T22: 0.2022
REMARK 3 T33: 0.1280 T12: 0.0249
REMARK 3 T13: -0.0365 T23: 0.0065
REMARK 3 L TENSOR
REMARK 3 L11: 3.6755 L22: 4.3271
REMARK 3 L33: 1.3098 L12: 0.5804
REMARK 3 L13: -0.2274 L23: 0.0834
REMARK 3 S TENSOR
REMARK 3 S11: -0.0405 S12: 0.2137 S13: -0.1249
REMARK 3 S21: 0.0643 S22: 0.1065 S23: -0.0195
REMARK 3 S31: -0.0870 S32: -0.1363 S33: -0.0661
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 218 A 286
REMARK 3 ORIGIN FOR THE GROUP (A): 26.2595 -61.0863 -7.9220
REMARK 3 T TENSOR
REMARK 3 T11: 0.1314 T22: 0.2277
REMARK 3 T33: 0.1309 T12: 0.0180
REMARK 3 T13: -0.0652 T23: 0.0218
REMARK 3 L TENSOR
REMARK 3 L11: 8.2094 L22: 1.9513
REMARK 3 L33: 1.2574 L12: 1.0872
REMARK 3 L13: -0.3681 L23: 0.5206
REMARK 3 S TENSOR
REMARK 3 S11: -0.0846 S12: 0.6317 S13: -0.5315
REMARK 3 S21: -0.1430 S22: 0.0944 S23: 0.0081
REMARK 3 S31: -0.0845 S32: -0.1204 S33: -0.0098
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 287 A 358
REMARK 3 ORIGIN FOR THE GROUP (A): 33.3112 -48.8521 18.8336
REMARK 3 T TENSOR
REMARK 3 T11: 0.4551 T22: 0.2334
REMARK 3 T33: 0.0653 T12: -0.2273
REMARK 3 T13: -0.0426 T23: 0.0906
REMARK 3 L TENSOR
REMARK 3 L11: 16.5909 L22: 8.0455
REMARK 3 L33: 4.3401 L12: 8.6357
REMARK 3 L13: 0.6684 L23: -0.0739
REMARK 3 S TENSOR
REMARK 3 S11: 0.7178 S12: -0.8679 S13: -0.1833
REMARK 3 S21: 0.8022 S22: -0.2921 S23: 0.1702
REMARK 3 S31: 0.0987 S32: -0.5027 S33: -0.4256
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 359 A 411
REMARK 3 ORIGIN FOR THE GROUP (A): 51.3363 -36.4201 7.1805
REMARK 3 T TENSOR
REMARK 3 T11: 0.3107 T22: 0.1338
REMARK 3 T33: 0.2559 T12: -0.1218
REMARK 3 T13: -0.0862 T23: -0.0175
REMARK 3 L TENSOR
REMARK 3 L11: 5.7065 L22: 4.6775
REMARK 3 L33: 2.8978 L12: 2.1995
REMARK 3 L13: 0.7051 L23: 3.1041
REMARK 3 S TENSOR
REMARK 3 S11: 0.3240 S12: -0.2211 S13: 0.0830
REMARK 3 S21: 0.1365 S22: -0.0696 S23: -0.2316
REMARK 3 S31: -0.0657 S32: 0.0972 S33: -0.2544
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 412 A 577
REMARK 3 ORIGIN FOR THE GROUP (A): 75.7633 -69.8223 -2.9358
REMARK 3 T TENSOR
REMARK 3 T11: 0.1899 T22: 0.4195
REMARK 3 T33: 0.3667 T12: 0.0262
REMARK 3 T13: -0.1177 T23: -0.1769
REMARK 3 L TENSOR
REMARK 3 L11: 2.6770 L22: 5.1961
REMARK 3 L33: 0.1998 L12: -2.4041
REMARK 3 L13: 0.7151 L23: -0.6781
REMARK 3 S TENSOR
REMARK 3 S11: 0.2345 S12: 0.2316 S13: 0.1223
REMARK 3 S21: 0.1765 S22: -0.2078 S23: -0.2930
REMARK 3 S31: 0.0754 S32: 0.1016 S33: -0.0267
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 578 A 612
REMARK 3 ORIGIN FOR THE GROUP (A): 87.7556-107.7472 13.5425
REMARK 3 T TENSOR
REMARK 3 T11: 0.4650 T22: 0.2168
REMARK 3 T33: 0.8520 T12: -0.1876
REMARK 3 T13: -0.2431 T23: 0.0172
REMARK 3 L TENSOR
REMARK 3 L11: 5.0475 L22: 11.9514
REMARK 3 L33: 12.3448 L12: -2.3883
REMARK 3 L13: -0.3983 L23: -1.5711
REMARK 3 S TENSOR
REMARK 3 S11: -0.5047 S12: 0.0697 S13: -0.9060
REMARK 3 S21: 0.7328 S22: 0.2663 S23: 0.3935
REMARK 3 S31: 0.8598 S32: -0.6304 S33: 0.2384
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 4GFJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-12.
REMARK 100 THE DEPOSITION ID IS D_1000074118.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-JUN-10
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19283
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910
REMARK 200 RESOLUTION RANGE LOW (A) : 29.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 6.200
REMARK 200 R MERGE (I) : 0.06900
REMARK 200 R SYM (I) : 0.07600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.91
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.04
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : 6.30
REMARK 200 R MERGE FOR SHELL (I) : 0.56600
REMARK 200 R SYM FOR SHELL (I) : 0.51900
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 2CSB
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH 7, 0.1 M KCL, 0.01 M
REMARK 280 MGCL2, AND 15% PEG 400, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 303K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+5/6
REMARK 290 6555 X-Y,X,Z+1/6
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.40900
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.81800
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.11350
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.52250
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.70450
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 ALA A 613
REMARK 465 ALA A 614
REMARK 465 GLU A 615
REMARK 465 ILE A 616
REMARK 465 LYS A 617
REMARK 465 GLY A 618
REMARK 465 PRO A 619
REMARK 465 GLU A 620
REMARK 465 PHE A 621
REMARK 465 LYS A 622
REMARK 465 PHE A 623
REMARK 465 LEU A 624
REMARK 465 LEU A 625
REMARK 465 ASN A 626
REMARK 465 ILE A 627
REMARK 465 GLU A 628
REMARK 465 GLY A 629
REMARK 465 VAL A 630
REMARK 465 GLY A 631
REMARK 465 PRO A 632
REMARK 465 LYS A 633
REMARK 465 LEU A 634
REMARK 465 ALA A 635
REMARK 465 GLU A 636
REMARK 465 ARG A 637
REMARK 465 ILE A 638
REMARK 465 LEU A 639
REMARK 465 GLU A 640
REMARK 465 ALA A 641
REMARK 465 VAL A 642
REMARK 465 ASP A 643
REMARK 465 TYR A 644
REMARK 465 ASP A 645
REMARK 465 LEU A 646
REMARK 465 GLU A 647
REMARK 465 ARG A 648
REMARK 465 LEU A 649
REMARK 465 ALA A 650
REMARK 465 SER A 651
REMARK 465 LEU A 652
REMARK 465 ASN A 653
REMARK 465 PRO A 654
REMARK 465 GLU A 655
REMARK 465 GLU A 656
REMARK 465 LEU A 657
REMARK 465 ALA A 658
REMARK 465 GLU A 659
REMARK 465 LYS A 660
REMARK 465 VAL A 661
REMARK 465 GLU A 662
REMARK 465 GLY A 663
REMARK 465 LEU A 664
REMARK 465 GLY A 665
REMARK 465 GLU A 666
REMARK 465 GLU A 667
REMARK 465 LEU A 668
REMARK 465 ALA A 669
REMARK 465 GLU A 670
REMARK 465 ARG A 671
REMARK 465 VAL A 672
REMARK 465 VAL A 673
REMARK 465 TYR A 674
REMARK 465 ALA A 675
REMARK 465 ALA A 676
REMARK 465 ARG A 677
REMARK 465 GLU A 678
REMARK 465 ARG A 679
REMARK 465 VAL A 680
REMARK 465 GLU A 681
REMARK 465 SER A 682
REMARK 465 ARG A 683
REMARK 465 ARG A 684
REMARK 465 LYS A 685
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ARG A 83 49.54 37.22
REMARK 500 VAL A 133 -81.23 -115.02
REMARK 500 ALA A 167 -109.57 -150.67
REMARK 500 ASN A 195 103.22 -163.32
REMARK 500 LYS A 282 -70.25 -21.29
REMARK 500 GLU A 375 -53.77 70.74
REMARK 500 SER A 451 15.66 -69.62
REMARK 500 LEU A 555 57.69 27.67
REMARK 500 PHE A 557 -146.31 -129.81
REMARK 500 ALA A 575 -68.08 -97.27
REMARK 500 SER A 590 -60.70 -106.63
REMARK 500 LEU A 591 -41.91 118.38
REMARK 500 ASP A 602 49.77 -70.10
REMARK 500 GLU A 605 -157.73 61.37
REMARK 500 ALA A 608 94.64 -69.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 704 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 161 OE2
REMARK 620 2 GLU A 161 OE1 63.6
REMARK 620 3 HIS A 246 NE2 103.0 96.5
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 704
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3M7G RELATED DB: PDB
REMARK 900 STRUCTURE OF TOPOISOMERASE DOMAIN OF TOPOISOMERASE V PROTEIN
REMARK 900 RELATED ID: 3M7D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE
REMARK 900 V IN THE PRESENCE OF DIOXANE
REMARK 900 RELATED ID: 3M6Z RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF AN N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE
REMARK 900 V IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE
REMARK 900 RELATED ID: 3M6K RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF N-TERMINAL 44 KDA FRAGMENT OF TOPOISOMERASE V
REMARK 900 IN THE PRESENCE OF GUANIDIUM HYDROCHLORIDE
REMARK 900 RELATED ID: 2CSB RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TOPOISOMERASE V FROM METHANOPYRUS KANDLERI (61
REMARK 900 KDA FRAGMENT)
REMARK 900 RELATED ID: 2CSD RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF TOPOISOMERASE V (61 KDA FRAGMENT)
DBREF 4GFJ A 1 685 UNP F1SVL0 F1SVL0_METKA 1 685
SEQRES 1 A 685 MET ALA LEU VAL TYR ASP ALA GLU PHE VAL GLY SER GLU
SEQRES 2 A 685 ARG GLU PHE GLU GLU GLU ARG GLU THR PHE LEU LYS GLY
SEQRES 3 A 685 VAL LYS ALA TYR ASP GLY VAL LEU ALA THR ARG TYR LEU
SEQRES 4 A 685 MET GLU ARG SER SER SER ALA LYS ASN ASP GLU GLU LEU
SEQRES 5 A 685 LEU GLU LEU HIS GLN ASN PHE ILE LEU LEU THR GLY SER
SEQRES 6 A 685 TYR ALA CYS SER ILE ASP PRO THR GLU ASP ARG TYR GLN
SEQRES 7 A 685 ASN VAL ILE VAL ARG GLY VAL ASN PHE ASP GLU ARG VAL
SEQRES 8 A 685 GLN ARG LEU SER THR GLY GLY SER PRO ALA ARG TYR ALA
SEQRES 9 A 685 ILE VAL TYR ARG ARG GLY TRP ARG ALA ILE ALA LYS ALA
SEQRES 10 A 685 LEU ASP ILE ASP GLU GLU ASP VAL PRO ALA ILE GLU VAL
SEQRES 11 A 685 ARG ALA VAL LYS ARG ASN PRO LEU GLN PRO ALA LEU TYR
SEQRES 12 A 685 ARG ILE LEU VAL ARG TYR GLY ARG VAL ASP LEU MET PRO
SEQRES 13 A 685 VAL THR VAL ASP GLU VAL PRO PRO GLU MET ALA GLY GLU
SEQRES 14 A 685 PHE GLU ARG LEU ILE GLU ARG TYR ASP VAL PRO ILE ASP
SEQRES 15 A 685 GLU LYS GLU GLU ARG ILE LEU GLU ILE LEU ARG GLU ASN
SEQRES 16 A 685 PRO TRP THR PRO HIS ASP GLU ILE ALA ARG ARG LEU GLY
SEQRES 17 A 685 LEU SER VAL SER GLU VAL GLU GLY GLU LYS ASP PRO GLU
SEQRES 18 A 685 SER SER GLY ILE TYR SER LEU TRP SER ARG VAL VAL VAL
SEQRES 19 A 685 ASN ILE GLU TYR ASP GLU ARG THR ALA LYS ARG HIS VAL
SEQRES 20 A 685 LYS ARG ARG ASP ARG LEU LEU GLU GLU LEU TYR GLU HIS
SEQRES 21 A 685 LEU GLU GLU LEU SER GLU ARG TYR LEU ARG HIS PRO LEU
SEQRES 22 A 685 THR ARG ARG TRP ILE VAL GLU HIS LYS ARG ASP ILE MET
SEQRES 23 A 685 ARG ARG TYR LEU GLU GLN ARG ILE VAL GLU CYS ALA LEU
SEQRES 24 A 685 LYS LEU GLN ASP ARG TYR GLY ILE ARG GLU ASP VAL ALA
SEQRES 25 A 685 LEU CYS LEU ALA ARG ALA PHE ASP GLY SER ILE SER MET
SEQRES 26 A 685 ILE ALA THR THR PRO TYR ARG THR LEU LYS ASP VAL CYS
SEQRES 27 A 685 PRO ASP LEU THR LEU GLU GLU ALA LYS SER VAL ASN ARG
SEQRES 28 A 685 THR LEU ALA THR LEU ILE ASP GLU HIS GLY LEU SER PRO
SEQRES 29 A 685 ASP ALA ALA ASP GLU LEU ILE GLU HIS PHE GLU SER ILE
SEQRES 30 A 685 ALA GLY ILE LEU ALA THR ASP LEU GLU GLU ILE GLU ARG
SEQRES 31 A 685 MET TYR GLU GLU GLY ARG LEU SER GLU GLU ALA TYR ARG
SEQRES 32 A 685 ALA ALA VAL GLU ILE GLN LEU ALA GLU LEU THR LYS LYS
SEQRES 33 A 685 GLU GLY VAL GLY ARG LYS THR ALA GLU ARG LEU LEU ARG
SEQRES 34 A 685 ALA PHE GLY ASN PRO GLU ARG VAL LYS GLN LEU ALA ARG
SEQRES 35 A 685 GLU PHE GLU ILE GLU LYS LEU ALA SER VAL GLU GLY VAL
SEQRES 36 A 685 GLY GLU ARG VAL LEU ARG SER LEU VAL PRO GLY TYR ALA
SEQRES 37 A 685 SER LEU ILE SER ILE ARG GLY ILE ASP ARG GLU ARG ALA
SEQRES 38 A 685 GLU ARG LEU LEU LYS LYS TYR GLY GLY TYR SER LYS VAL
SEQRES 39 A 685 ARG GLU ALA GLY VAL GLU GLU LEU ARG GLU ASP GLY LEU
SEQRES 40 A 685 THR ASP ALA GLN ILE ARG GLU LEU LYS GLY LEU LYS THR
SEQRES 41 A 685 LEU GLU SER ILE VAL GLY ASP LEU GLU LYS ALA ASP GLU
SEQRES 42 A 685 LEU LYS ARG LYS TYR GLY SER ALA SER ALA VAL ARG ARG
SEQRES 43 A 685 LEU PRO VAL GLU GLU LEU ARG GLU LEU GLY PHE SER ASP
SEQRES 44 A 685 ASP GLU ILE ALA GLU ILE LYS GLY ILE PRO LYS LYS LEU
SEQRES 45 A 685 ARG GLU ALA PHE ASP LEU GLU THR ALA ALA GLU LEU TYR
SEQRES 46 A 685 GLU ARG TYR GLY SER LEU LYS GLU ILE GLY ARG ARG LEU
SEQRES 47 A 685 SER TYR ASP ASP LEU LEU GLU LEU GLY ALA THR PRO LYS
SEQRES 48 A 685 ALA ALA ALA GLU ILE LYS GLY PRO GLU PHE LYS PHE LEU
SEQRES 49 A 685 LEU ASN ILE GLU GLY VAL GLY PRO LYS LEU ALA GLU ARG
SEQRES 50 A 685 ILE LEU GLU ALA VAL ASP TYR ASP LEU GLU ARG LEU ALA
SEQRES 51 A 685 SER LEU ASN PRO GLU GLU LEU ALA GLU LYS VAL GLU GLY
SEQRES 52 A 685 LEU GLY GLU GLU LEU ALA GLU ARG VAL VAL TYR ALA ALA
SEQRES 53 A 685 ARG GLU ARG VAL GLU SER ARG ARG LYS
HET GOL A 701 6
HET GOL A 702 6
HET GOL A 703 6
HET ZN A 704 1
HETNAM GOL GLYCEROL
HETNAM ZN ZINC ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 GOL 3(C3 H8 O3)
FORMUL 5 ZN ZN 2+
FORMUL 6 HOH *4(H2 O)
HELIX 1 1 SER A 12 GLU A 41 1 30
HELIX 2 2 SER A 43 ASN A 48 1 6
HELIX 3 3 ASP A 49 SER A 69 1 21
HELIX 4 4 PHE A 87 LEU A 94 1 8
HELIX 5 5 SER A 99 VAL A 106 1 8
HELIX 6 6 GLY A 110 LEU A 118 1 9
HELIX 7 7 ASP A 121 VAL A 125 5 5
HELIX 8 8 GLN A 139 TYR A 149 1 11
HELIX 9 9 PRO A 163 ALA A 167 5 5
HELIX 10 10 PHE A 170 ARG A 176 1 7
HELIX 11 11 ASP A 182 ASN A 195 1 14
HELIX 12 12 PRO A 199 GLY A 208 1 10
HELIX 13 13 SER A 210 GLY A 216 1 7
HELIX 14 14 GLY A 224 ASN A 235 1 12
HELIX 15 15 ASP A 239 GLU A 266 1 28
HELIX 16 16 THR A 274 ARG A 304 1 31
HELIX 17 17 ARG A 308 PHE A 319 1 12
HELIX 18 18 SER A 322 THR A 328 1 7
HELIX 19 19 PRO A 330 CYS A 338 1 9
HELIX 20 20 THR A 342 ASN A 350 1 9
HELIX 21 21 ASN A 350 GLU A 359 1 10
HELIX 22 22 SER A 363 GLU A 375 1 13
HELIX 23 23 SER A 376 ALA A 382 1 7
HELIX 24 24 ASP A 384 GLU A 394 1 11
HELIX 25 25 SER A 398 LYS A 415 1 18
HELIX 26 26 GLY A 420 GLY A 432 1 13
HELIX 27 27 ASN A 433 GLU A 443 1 11
HELIX 28 28 GLU A 445 SER A 451 1 7
HELIX 29 29 GLY A 456 VAL A 464 1 9
HELIX 30 30 GLY A 466 SER A 472 1 7
HELIX 31 31 ASP A 477 GLY A 489 1 13
HELIX 32 32 GLY A 490 ALA A 497 1 8
HELIX 33 33 GLY A 498 ASP A 505 1 8
HELIX 34 34 THR A 508 GLY A 517 1 10
HELIX 35 35 LEU A 518 VAL A 525 1 8
HELIX 36 36 ASP A 527 TYR A 538 1 12
HELIX 37 37 SER A 540 LEU A 547 1 8
HELIX 38 38 PRO A 548 GLU A 554 1 7
HELIX 39 39 SER A 558 GLY A 567 1 10
HELIX 40 40 PRO A 569 PHE A 576 1 8
HELIX 41 41 ASP A 577 GLY A 589 1 13
HELIX 42 42 LYS A 592 ARG A 597 5 6
HELIX 43 43 LEU A 598 ASP A 602 5 5
HELIX 44 44 ALA A 608 ALA A 612 5 5
SHEET 1 A 3 ASP A 6 PHE A 9 0
SHEET 2 A 3 TYR A 77 VAL A 82 -1 O ILE A 81 N ASP A 6
SHEET 3 A 3 VAL A 85 ASN A 86 -1 O VAL A 85 N VAL A 82
SSBOND 1 CYS A 314 CYS A 338 1555 1555 2.04
LINK OE2 GLU A 161 ZN ZN A 704 1555 1555 2.05
LINK OE1 GLU A 161 ZN ZN A 704 1555 1555 2.06
LINK NE2 HIS A 246 ZN ZN A 704 1555 1555 2.16
SITE 1 AC1 3 VAL A 133 LYS A 134 GOL A 703
SITE 1 AC2 4 GLU A 221 ASP A 384 PHE A 431 GLY A 432
SITE 1 AC3 6 ARG A 108 ARG A 131 VAL A 133 ARG A 293
SITE 2 AC3 6 SER A 322 GOL A 701
SITE 1 AC4 3 GLU A 161 GLU A 194 HIS A 246
CRYST1 161.634 161.634 58.227 90.00 90.00 120.00 P 61 6
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006187 0.003572 0.000000 0.00000
SCALE2 0.000000 0.007144 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017174 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
